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Buonaiuto DM, Davies TJ, Collins SC, Wolkovich EM. Ecological drivers of flower-leaf sequences: aridity and proxies for pollinator attraction select for flowering-first in the American plums. THE NEW PHYTOLOGIST 2024. [PMID: 38561636 DOI: 10.1111/nph.19685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Across temperate forests, many tree species produce flowers before their leaves emerge. This flower-leaf phenological sequence, known as hysteranthy, is generally described as an adaptation for wind pollination. However, this explanation does not address why hysteranthy is also common in biotically pollinated taxa. We quantified flower-leaf sequence variation in the American plums (Prunus, subg. Prunus sect. Prunocerasus), a clade of insect-pollinated trees, using herbaria specimens and Bayesian hierarchical modeling. We tested two common, but rarely interrogated hypotheses - that hysteranthy confers aridity tolerance and/or pollinator visibility - by modeling the associations between hysteranthy and related traits. To understand how these phenology-trait associations were sensitive to taxonomic scale and flower-leaf sequence classification, we then extended these analyses to all Prunus species in North America. Our findings across two taxonomic levels support the hypotheses that hysteranthy may help temporally partition hydraulic demand to reduce water stress and increase pollinator visibility - thereby reducing selective pressure on inflorescence size. Our results provide foundational insights into the evolution of flower-leaf sequences in the genus Prunus, with implications for understanding these patterns in biotically pollinated plants in general. Our approach suggests a path to advance these hypotheses to other clades, but teasing out drivers fully will require new experiments.
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Affiliation(s)
- D M Buonaiuto
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA
- Arnold Arboretum of Harvard University, Boston, MA, 02131, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - T J Davies
- Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - S C Collins
- Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - E M Wolkovich
- Arnold Arboretum of Harvard University, Boston, MA, 02131, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Youssef D, El-Bakatoushi R, Elframawy A, El-Sadek L, Badan GE. Molecular phylogenetic study of flavonoids in medicinal plants: a case study family Apiaceae. JOURNAL OF PLANT RESEARCH 2023; 136:305-322. [PMID: 36853579 PMCID: PMC10126080 DOI: 10.1007/s10265-023-01442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/12/2023] [Indexed: 05/25/2023]
Abstract
The current study examined the phylogenetic pattern of medicinal species of the family Apiaceae based on flavonoid groups production, as well as the overall mechanism of the key genes involved in flavonol and flavone production. Thirteen species of the family Apiaceae were used, including Eryngium campestre from the subfamily Saniculoideae, as well as Cuminum cyminum, Carum carvi, Coriandrum sativum, Apium graveolens, Petroselinum crispum, Pimpinella anisum, Anethum graveolens, Foeniculum vulgare, Daucus carota, Ammi majus, Torilis arvensis, and Deverra tortuosa from the subfamily Apioideae. The seeds were cultivated, and the leaves were collected to estimate flavonoids and their groups, physiological factors, transcription levels of flavonol and flavone production-related genes. The phylogenetic relationship between the studied species was established using the L-ribosomal 16 (rpl16) chloroplast gene. The results revealed that the studied species were divided into two patterns: six plant species, E. campestre, C. carvi, C. sativum, P. anisum, An. graveolens, and D. carota, contained low content of flavonoids, while the other seven species had high content. This pattern of flavonoids production coincided with the phylogenetic relationships between the studied species. In contrast, the phylogeny of the flavonol and flavone synthase genes was incompatible with the quantitative production of their products. The study concluded that the increment in the production of flavonol depends on the high expression of chalcone synthase, chalcone isomerase, flavanone 3 hydroxylase, flavonol synthase, the increase of Abscisic acid, sucrose, and phenyl ammonia lyase, while flavone mainly depends on evolution and on the high expression of the flavone synthase gene.
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Affiliation(s)
- Dalia Youssef
- Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, EgyptAlexandria, El-Shatby, 21526, Egypt.
| | - Ranya El-Bakatoushi
- Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, EgyptAlexandria, El-Shatby, 21526, Egypt
| | - Asmaa Elframawy
- Nucleic Acids Research Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), City for Scientific Research and Technological Applications, Borg El-Arab, Alexandria, 21933, Egypt
| | - Laila El-Sadek
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Camp Caesar, Alexandria, 21525, Egypt
| | - Ghada El Badan
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Camp Caesar, Alexandria, 21525, Egypt
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Wan T, Qiao BX, Zhou J, Shao KS, Pan LY, An F, He XS, Liu T, Li PK, Cai YL. Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1070600. [PMID: 36938043 PMCID: PMC10022824 DOI: 10.3389/fpls.2023.1070600] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens 'Gisela 6', and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.
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Affiliation(s)
- Tian Wan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Bai-xue Qiao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Jing Zhou
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ke-sen Shao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Liu-yi Pan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Feng An
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Xu-sheng He
- College of Natural Resources and Environment, Northwest Agriculture & Forestry University, Yangling, China
| | - Tao Liu
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ping-ke Li
- Center of Experimental Station, Northwest Agriculture & Forestry University, Yangling, China
| | - Yu-liang Cai
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
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Abstract
Plums are a large group of closely related stone fruit species and hybrids of worldwide economic importance and diffusion. This review deals with the main aspects concerning plum agrobiodiversity and its relationship with current and potential contributions offered by breeding in enhancing plum varieties. The most recent breeding achievements are revised according to updated information proceeding from relevant scientific reports and official inventories of plum genetic resources. A special emphasis has been given to the potential sources of genetic traits of interest for breeding programs as well as to the need for efficient and coordinated efforts aimed at efficaciously preserving the rich and underexploited extant plum agrobiodiversity. The specific objective of this review was to: (i) analyze and possibly evaluate the degree of biodiversity existing in the cultivated plum germplasm, (ii) examine the set of traits of prominent agronomic and pomological interest currently targeted by the breeders, and (iii) determine how and to what extent this germplasm was appropriately exploited in breeding programs or could represent concrete prospects for the future.
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Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
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Zhang X, Jiang Z, Yusupov Z, Zhang M, Zhang D, Tojibaev K, Meng Y, Deng T. Prunus sunhangii: A new species of Prunus from central China. PLANT DIVERSITY 2019; 41:19-25. [PMID: 30931414 PMCID: PMC6412158 DOI: 10.1016/j.pld.2019.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/20/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
A new species of Rosaceae from Central China, Prunus sunhangii D. G. Zhang & T. Deng, sp. nov. , is described and illustrated. The new species is placed in Prunus subgenus Cerasus by flower and fruit characteristics. It is most similar to Prunus cerasoides, but differs by having longitudinally 2-lobed apical petals, an acuminate leaf apex, 17-25 stamens, white petals, dark black drupes, brown hypanthium, and different phenology. The phylogenetic placement of this species was assessed based on morphological and molecular data. Molecular analysis (cpDNA + ITS) corroborated its placement in subgenus Cerasus, specifically Prunus section Serrula.
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Affiliation(s)
- Xiaoshuang Zhang
- Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, Hunan, China
| | - Zhilin Jiang
- Puer University, Puer 665000, Yunnan, China
- Institute of Comparative Study of Traditional Materia Medica, Institutes of Integrative Medicine, Fudan University, Shanghai, 200040, China
| | - Ziyoviddin Yusupov
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Central Herbarium of Uzbekistan, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Menghua Zhang
- Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, Hunan, China
| | - Daigui Zhang
- Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, Hunan, China
| | - Komiljon Tojibaev
- Central Herbarium of Uzbekistan, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, Hunan, China
| | - Tao Deng
- Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, Jishou 416000, Hunan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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Tomasello S, Stuessy TF, Oberprieler C, Heubl G. Ragweeds and relatives: Molecular phylogenetics of Ambrosiinae (Asteraceae). Mol Phylogenet Evol 2018; 130:104-114. [PMID: 30292693 DOI: 10.1016/j.ympev.2018.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 02/07/2023]
Abstract
Ambrosiinae are one of the most distinct subtribes in the Heliantheae alliance (Asteraceae), mainly due to specialization toward wind pollination. Taxa of the subtribe are principally native to the Americas, although some species have attained a cosmopolitan distribution. Members of subtribe Engelmanniinae are considered close to Ambrosiinae, due to shared morphological traits. However, the placement of Ambrosiinae within the Heliantheae alliance has not yet been corroborated by phylogenetic analyses. In the present study, we test the circumscription of subtribe Ambrosiinae and examine relationships among its genera. We used sequence information from three plastid (psbA-trnH, trnQ-rps16 and trnL-F) and two nuclear (ITS and D35) marker regions. Phylogenetic inference analyses were conducted, applying Bayesian Inference (BI) and Maximum Likelihood (ML). Subtribe Ambrosiinae is found monophyletic or nearly so in all analyses. The genera Dugesia and Rojasianthe (previously considered part of subtribe Engelmanniinae) in some cases cluster together with Ambrosiinae; these genera are clearly not part of Engelmanniinae. Within Ambrosiinae, the genera Parthenium and Parthenice occupy basal positions, whereas members of the genus Ambrosia are the most derived representatives of the subtribe. Previous subdivision of Ambrosiinae into "Iveae" (members having androgynous capitula and free achenes) and "Ambrosieae" (genera with unisexual heads and achenes enclosed in burs) is not corroborated. Results also allow consideration of relationships among species and subgeneric groups within Parthenium, Iva, and Ambrosia.
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Affiliation(s)
- Salvatore Tomasello
- Systematic Botany and Mycology, Department Biology I, Ludwig-Maximilians-University Munich (LMU) and GeoBio-Center (LMU), Munich, Germany.
| | - Tod F Stuessy
- Herbarium and Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA; Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstrasse 31, 93040 Regensburg, Germany
| | - Günther Heubl
- Systematic Botany and Mycology, Department Biology I, Ludwig-Maximilians-University Munich (LMU) and GeoBio-Center (LMU), Munich, Germany
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Taxa of Rosaceae of the Ukrainian flora: position in a new system of the family according to molecular phylogenetic data. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Vander Mijnsbrugge K, Turcsán A, Depypere L, Steenackers M. Variance, Genetic Control, and Spatial Phenotypic Plasticity of Morphological and Phenological Traits in Prunus spinosa and Its Large Fruited Forms ( P. x fruticans). FRONTIERS IN PLANT SCIENCE 2016; 7:1641. [PMID: 27857718 PMCID: PMC5093327 DOI: 10.3389/fpls.2016.01641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
Prunus spinosa is a highly esteemed shrub in forest and landscape plantings. Shrubs with larger organs occur often and are considered either as large fruited forms of P. spinosa or as P. x fruticans, involving a hybridization process with the ancient cultivated P. insititia (crop-to-wild gene flow). As climate change may augment hybridization processes in the future, a hybrid origin is important to detect. In addition, studying crop-to-wild gene flow can give insights in putative consequences for the wild populations. We studied the P. spinosa-P. x fruticans group, focusing on morphology and phenology in three experimental plantations. Two plantings harbored cuttings of P. spinosa (clone plantations). A third plantation comprised of a half-sib offspring from a population with both P. spinosa and P. x fruticans (family plantation). Several results point to a hybridization process as the origin of P. x fruticans. The clone plantation revealed endocarp traits to be more genetically controlled than fruit size, while this was the opposite in the family plantation, suggesting the control of fruit size being derived from the putative P. insititia parent. Bud burst, flower opening, and leaf fall were genetically controlled in the clone plantation, whereas in the family plantation intrafamily variability was remarkably large for the bud burst and leaf fall, but not for the flower opening. This suggests there is a reduced genetic control for the first two phenophases, possibly caused by historic hybridization events. Pubescence on the long shoot leaves in the family plantation deviated from the short shoot leaves on the same plants and from long and short shoot leaves in the clone plantation, suggesting again a P. insititia origin. Finally, we quantified spatial phenotypic plasticity, indicating how P. spinosa may react in a changing environment. In contrast to the bud burst and leaf fall, flower opening did not demonstrate plasticity. The fruit size was diminished at the growth site with the shortest growing season while interestingly, the leaf width was enlarged. Leaf size traits appeared more plastic on the long shoots compared to the short shoots, although partitioning of variance did not display a lesser genetic control.
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Affiliation(s)
| | - Arion Turcsán
- Department of Forest Genetic Resources, Research Institute for Nature and ForestGeraardsbergen, Belgium
- Department of Biometrics and Agricultural Informatics, Szent István UniversityBudapest, Hungary
- Department of Forest Reproductive Material and Plantation Management, Institute of Silviculture and Forest Protection, West-Hungarian UniversitySopron, Hungary
| | - Leander Depypere
- Formerly affiliated with the Department of Biology, Research Group Spermatophytes, Ghent UniversityGhent, Belgium
| | - Marijke Steenackers
- Department of Forest Genetic Resources, Research Institute for Nature and ForestGeraardsbergen, Belgium
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Shaw J, Shafer HL, Leonard OR, Kovach MJ, Schorr M, Morris AB. Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV. AMERICAN JOURNAL OF BOTANY 2014; 101:1987-2004. [PMID: 25366863 DOI: 10.3732/ajb.1400398] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels. METHODS We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level. KEY RESULTS Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL((UAG)), ndhC-trnV((UAC)), 5'rps16-trnQ((UUG)), psbE-petL, trnT((GGU))-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is ∼2.5, which may be too little to access the full discriminating power of this genome. CONCLUSIONS Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.
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Affiliation(s)
- Joey Shaw
- Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA Botanical Research Institute of Texas, Fort Worth, Texas USA
| | - Hayden L Shafer
- Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA
| | - O Rayne Leonard
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA
| | - Margaret J Kovach
- Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA
| | - Mark Schorr
- Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA
| | - Ashley B Morris
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA
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Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae). Mol Phylogenet Evol 2014; 76:34-48. [DOI: 10.1016/j.ympev.2014.02.024] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/15/2013] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
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Shi S, Li J, Sun J, Yu J, Zhou S. Phylogeny and classification of Prunus sensu lato (Rosaceae). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:1069-79. [PMID: 23945216 DOI: 10.1111/jipb.12095] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/22/2013] [Indexed: 05/26/2023]
Abstract
The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü & L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed.
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Affiliation(s)
- Shuo Shi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100043, China
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Navarro-Pérez ML, López J, Fernández-Mazuecos M, Rodríguez-Riaño T, Vargas P, Ortega-Olivencia A. The role of birds and insects in pollination shifts of Scrophularia (Scrophulariaceae). Mol Phylogenet Evol 2013; 69:239-54. [PMID: 23756207 DOI: 10.1016/j.ympev.2013.05.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 05/17/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
The mixed vertebrate-insect pollination system is rare in Holarctic plants. Phylogenetic relationships of 116 Scrophularia taxa were investigated based on two plastid (ndhF and trnL-trnF) and one nuclear (ITS) DNA regions. A wider time-calibrated analysis of ndhF sequences of the Lamiales revealed that Scrophularia diverged as early as in the Miocene (<22 Ma). Results of maximum-likelihood optimizations supported wasp pollination as the ancestral pollination system from which other systems derived (hoverfly, mixed vertebrate-insect and bird systems). Four origins for a mixed vertebrate-insect (MVI) pollination system were inferred, in which two western Mediterranean species (S. sambucifolia and S. grandiflora) and two island species (the Tirrenian S. trifoliata and the Canarian S. calliantha) were involved. S. calliantha is the only species in which a more complex MVI system, including pollination by the lizard Gallotia stehlini, has evolved. In addition, bird (hummingbird) floral traits found in the New Mexican S. macrantha appear to have been independently acquired. In contrast, we failed to find evidence for an ancient role of hummingbirds in the evolution of European Scrophularia. Indeed, paleontological data revealed that extinction of European hummingbirds (30-32 Ma) occurred earlier than the divergence of European MVI lineages of Scrophularia. In conclusion, our results showed that a role of birds in pollination of Scrophularia may not have been effective in the Miocene-Pliocene, but bird pollination that shows its origin in the Pliocene-Pleistocene is still operating independently in different islands and continents.
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Affiliation(s)
- María L Navarro-Pérez
- Área de Botánica, Facultad de Ciencias, Universidad de Extremadura, Avda. de Elvas s.n., 06006 Badajoz, Spain.
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Weber MG, Keeler KH. The phylogenetic distribution of extrafloral nectaries in plants. ANNALS OF BOTANY 2013; 111:1251-61. [PMID: 23087129 PMCID: PMC3662505 DOI: 10.1093/aob/mcs225] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/19/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory. METHODS Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated. KEY RESULTS To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1-2 % of vascular plant species and approx. 21 % of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported. CONCLUSIONS EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the phylogenetic patterns of EFNs makes them powerful candidates for future work exploring the drivers of their evolutionary origins, shifts, and losses.
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Affiliation(s)
- Marjorie G Weber
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA.
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Liu XL, Wen J, Nie ZL, Johnson G, Liang ZS, Chang ZY. Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America. JOURNAL OF PLANT RESEARCH 2013; 126:351-361. [PMID: 23239308 DOI: 10.1007/s10265-012-0535-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 10/17/2012] [Indexed: 06/01/2023]
Abstract
Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59-6.15)-4.1 (95 % HPD 0.63-8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.
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Affiliation(s)
- Xiao-Lin Liu
- College of Life Science, Northwest Agriculture and Forest University, Yangling, Shaanxi, China.
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Kellner A, Ritz CM, Schlittenhardt P, Hellwig FH. Genetic differentiation in the genus Lithops L. (Ruschioideae, Aizoaceae) reveals a high level of convergent evolution and reflects geographic distribution. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:368-380. [PMID: 21309984 DOI: 10.1111/j.1438-8677.2010.00354.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Southern Africa is one of the hot spots for plant biodiversity, with ca. 80% of species endemic to this area. Rapid and recent radiations in Southern African plant genera were triggered by fine-scale differences in climate, topography and geology. The genus Lithops (Ruschioideae, Aizoaceae) contains 37 species and is widely distributed in Southern Africa. Species delimitation within the genus is challenging because the limited number of morphological characters in these reduced succulents varies intensely between populations, presumably as adaptations to local geological environments. We analysed phylogenetic relationships within Lithops using non-coding chloroplast DNA (trnS-trnG intergenic spacer), nuclear ribosomal internal transcribed spacer (nrITS) sequences and AFLP data. Genetic variability of the sequence data was very low, but AFLP data detected nine clades within Lithops that do not fit current morphology-based taxonomy. Two of these clades are separated by their distribution on the northern and eastern border of the distribution area, and four clades are found in the Gariep Centre in the estuary of the Orange River. Morphological similarities, especially colour of leaves, evolved repeatedly within the clades, thus we hypothesise that closely related species became adapted to different soil types in a mosaic-like geological environment. One-third of the species are found in the Gariep Centre, characterised by extremely diverse edaphic habitats.
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Affiliation(s)
- A Kellner
- Department of Systematic Botany, Justus-Liebig-University, Giessen, Germany
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17
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Zeng CX, Zhang YX, Triplett JK, Yang JB, Li DZ. Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Mol Phylogenet Evol 2010; 56:821-39. [DOI: 10.1016/j.ympev.2010.03.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/31/2010] [Accepted: 03/31/2010] [Indexed: 11/24/2022]
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18
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Chatrou LW, Escribano MP, Viruel MA, Maas JW, Richardson JE, Hormaza JI. Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics. Mol Phylogenet Evol 2009; 53:726-33. [DOI: 10.1016/j.ympev.2009.07.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 07/16/2009] [Accepted: 07/23/2009] [Indexed: 12/01/2022]
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Kumar S, Hahn FM, McMahan CM, Cornish K, Whalen MC. Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. BMC PLANT BIOLOGY 2009; 9:131. [PMID: 19917140 PMCID: PMC2784773 DOI: 10.1186/1471-2229-9-131] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 11/17/2009] [Indexed: 05/03/2023]
Abstract
BACKGROUND Parthenium argentatum (guayule) is an industrial crop that produces latex, which was recently commercialized as a source of latex rubber safe for people with Type I latex allergy. The complete plastid genome of P. argentatum was sequenced. The sequence provides important information useful for genetic engineering strategies. Comparison to the sequences of plastid genomes from three other members of the Asteraceae, Lactuca sativa, Guitozia abyssinica and Helianthus annuus revealed details of the evolution of the four genomes. Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines. RESULTS The complete plastid genome of P. argentatum is 152,803 bp. Based on the overall comparison of individual protein coding genes with those in L. sativa, G. abyssinica and H. annuus, we demonstrate that the P. argentatum chloroplast genome sequence is most closely related to that of H. annuus. Similar to chloroplast genomes in G. abyssinica, L. sativa and H. annuus, the plastid genome of P. argentatum has a large 23 kb inversion with a smaller 3.4 kb inversion, within the large inversion. Using the matK and psbA-trnH spacer chloroplast DNA barcodes, three of the four Parthenium species tested, P. tomentosum, P. hysterophorus and P. schottii, can be differentiated from P. argentatum. In addition, we identified lines within P. argentatum. CONCLUSION The genome sequence of the P. argentatum chloroplast will enrich the sequence resources of plastid genomes in commercial crops. The availability of the complete plastid genome sequence may facilitate transformation efficiency by using the precise sequence of endogenous flanking sequences and regulatory elements in chloroplast transformation vectors. The DNA barcoding study forms the foundation for genetic identification of commercially significant lines of P. argentatum that are important for producing latex.
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Affiliation(s)
- Shashi Kumar
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, 800 Buchanan Street, Albany CA 94710, USA
- Yulex Corporation, 37860 W Smith-Enke Road, Maricopa, AZ 85238-3010, USA
| | - Frederick M Hahn
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, 800 Buchanan Street, Albany CA 94710, USA
| | - Colleen M McMahan
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, 800 Buchanan Street, Albany CA 94710, USA
| | - Katrina Cornish
- Yulex Corporation, 37860 W Smith-Enke Road, Maricopa, AZ 85238-3010, USA
| | - Maureen C Whalen
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, 800 Buchanan Street, Albany CA 94710, USA
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Yuan YW, Olmstead RG. A species-level phylogenetic study of the Verbena complex (Verbenaceae) indicates two independent intergeneric chloroplast transfers. Mol Phylogenet Evol 2008; 48:23-33. [DOI: 10.1016/j.ympev.2008.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 03/17/2008] [Accepted: 04/05/2008] [Indexed: 11/30/2022]
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21
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Shneyer VS. On the species-specificity of DNA: Fifty years later. BIOCHEMISTRY (MOSCOW) 2007; 72:1377-84. [DOI: 10.1134/s0006297907120127] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Liu Q, Peterson PM, Columbus JT, Zhao N, Hao G, Zhang D. Inflorescence diversification in the "finger millet clade" (Chloridoideae, Poaceae): a comparison of molecular phylogeny and developmental morphology. AMERICAN JOURNAL OF BOTANY 2007; 94:1230-1247. [PMID: 21636489 DOI: 10.3732/ajb.94.7.1230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Within the Poaceae, inflorescence diversification and its bearing on phylogeny and evolution are exceedingly complex. We used phylogenetic information of the "finger millet clade," a group of grasses with digitate inflorescences, to study the inflorescence diversification. This clade appears monophyletic in the morphological and molecular phylogenetic analyses. Three well-supported clades are shown in our cpDNA-derived phylogeny, with clades I and III consisting of species of Chloris and Microchloa, respectively, and clade II including species of Cynodon, Dactyloctenium, and Eleusine. Variation appears at different times throughout development. Changes involving primordium number and arrangement occur very early, changes involving duration of primordium activity occur much later. Characters derived from the comparison of developmental sequences were optimized onto the most parsimonious tree. The developmental characters were congruent with the molecular phylogeny. Two developmental characters may not be homologous in the Chloris subclade and the Cynodon subclade.
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Affiliation(s)
- Qing Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Hughest CE, Eastwood RJ, Bailey CD. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philos Trans R Soc Lond B Biol Sci 2006; 361:211-25. [PMID: 16553318 PMCID: PMC1626539 DOI: 10.1098/rstb.2005.1735] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 08/12/2005] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from 'universal' gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous nongenic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.
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Affiliation(s)
- Colin E Hughest
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. AMERICAN JOURNAL OF BOTANY 2005; 92:142-66. [PMID: 21652394 DOI: 10.3732/ajb.92.1.142] [Citation(s) in RCA: 796] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.
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Affiliation(s)
- Joey Shaw
- Department of Botany, 437 Hesler Biology, University of Tennessee, Knoxville, Tennessee 37996 USA
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